Questions tagged [dna]

Deoxyribonucleic acid (DNA) is the carrier of genetic information, including for all known living organisms. The only known exceptions are RNA viruses.

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51 views

Changes in DNA and forensic cases

If DNA changes over time, how is it that forensic DNA gathered decades ago can be matched to a person today for solving crimes?
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Is presence of air necessary for silica gel to absorb moisture?

I am a biologist currently doing field work where I need to quickly dry leaf samples using silica gel crystals. I use the orange indicating kind that are 2-4mm in size. The setup is like this. I ...
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50 views

Is UV radiation more likely to cause mutations during mitosis?

According to Life: The Science of Biology (10th edition), UV radiation might cause the formation of pyrimidine dimers, which are the primary cause of skin cancer in humans. Are mutations more likely ...
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Genes of the electron transport chain

Where are the genes of proteins that make the electron transport chain of mitochondria?(are they in in the nucleus or they are in the dna of the mitochondria itself?) Thanks for this answering system ...
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How is it possible for phosphate to form two ester bonds in DNA replication?

I understand that in phosphodiester bond formation, two hydroxl groups on the phosphate molecule bind to the 3' and 5' OH groups on two independent pentose sugars. This is a condensation reaction, so ...
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155 views

How does DNA code for the actual *shape* of individual body parts/areas (NOT segments or Hox genes)?

Just to save the trouble - I am not asking for general information on how DNA codes for proteins and definitely not how Hox genes work. I have a very good understanding of the evolutionary process and ...
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How to convert enrichment/depletion to frequency for comparing deep sequencing to sequence profile?

I have two datasets, from different sources, that I need to compare. The first set is deep sequencing results of a directed evolution experiment, where I have the naive library and selected library ...
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38 views

Does every protein encoding gene necessarily have a transcription factor?

For instance, transcription factor gene A is responsible for activating gene B that encodes protein 1. However, it is possible for genes like gene B to encode proteins without having transcription ...
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How to preserve tissue DNA without using formalin?

Except using formalin to preserve human corpse for autopsy. I heard from the news that technique damages the DNA in the organs Question: Suppose corpse will be investigated next by another juridical ...
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How specific are Vitamin D promotors in the DNA?

As far as I understand there are genes that get regulated by the amount of Vitamin D that comes in contact with DNA. How specific are those promoters? Are there promotors that for example only get ...
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53 views

How diverse are the sperm cells of an individual male due to random mutations?

Due to the sheer number of sperm cells in an individual and the rate of mutations, are they likely to be incredibly diverse and encompass most of what we see across our species? For instance would it ...
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66 views

UV-lamp, DNA and RNA extraction lab

I'm equipping a lab room (~3x5 meters) that's supposed to be used for DNA and RNA extractions. I know about the basic safety precautions when working with RNA and DNA extraction (fresh gloves, ...
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215 views

Why is the Mongolian Horse superior in stamina?

I've heard a lot about the Mongolian Horse over the years, especially that it has more stamina than the Arabian Horse. It's a little smaller/lighter than an Arabian. Apparently the Mongol Horse can ...
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Do cells store information other than permanent (chromosome) information

The brain stores information in neurons (i.e. neural networks), and cells store information in DNA. But with DNA, this is permanent information. There is a lot of potential temporary information in ...
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47 views

DNA synthesis in nucleus

I read somewhere that according to a research, I don't remember what the date was, that our cells stop synthesising DNA around noon and restart it around the sunset. The research told that it was ...
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40 views

What percentage of a complete Denisovan genomes lives on in the union of the sets of overlapping pieces in extant humans

In studies like this one mapping out distributions around the world or the analysis described in this article (suggesting a contribution from a non-Denisovan but Denisovan-like unidentified hominin to ...
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32 views

What percentage of genome do slugs and scallops have in common?

We can know genetic distance of thousands of species. The OTT tree of life gives genetic distance for nearly all species. Is there a resource to compare the genomes of any sequenced animals to know ...
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605 views

DNA linking number, twist and writhe

The image below is taken from a molecular biology textbook. It is not clear to me that what is happening at the two writhe crossings matches up with the numbers provided. Is there a problem with ...
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What determines the differences between differentiated cells?

Given two multi-cellular species with obviously different phenotypes. The reason for the different phenotypes reflects their different DNA. However two types of cells in an adult organism may have ...
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Dyes that won’t bind to dna

I am looking for a dye that won’t bind to DNA. I want to add dye to proteinase K to make is visible when adding to clear buffer liquid samples. I need it to not bind to the DNA so it will be removed ...
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203 views

How do I go about traveling with DNA extract samples?

I am traveling from Fairbanks, Alaska to Vienna, Austria in six weeks and need to bring 10 very small (~50 ul) samples of extracted arctic ground squirrel DNA with me. I need to travel with these on ...
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What is the difference between average sperm epimutations and intersection sperm epimutations, in the context of the attached article?

The paper of interest is Manikkam et al. (2014). In research for a school Year 10 Science project, I came upon this article and the following two graphics. I don’t quite understand the difference ...
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330 views

why is DNA better for storing genetic info while RNA better for transmission of it?

I do know that RNA cannot be used for transmission since it is unstable, but how does it prove to be a better transmitter of genetic information?
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Multi-protein drug treatments

Apologies if this an obvious question - I am very new to this. I am, as of now, under the impression that multiple SNP variations interact to create multiple mutated proteins, which ultimately results ...
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Effect of UV radiation on retinoid (vitamin A) receptors in the skin

The retinoid receptors in the skin (face) can be disabled by UVA sun radiation as these study states : https://www.sciencedaily.com/releases/1999/03/990331063314.htm In this article it says the same :...
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Non-cavitating ultrasound for denaturation of short strands of DNA (~20 bp)?

I know that there is existing research on ultrasound-induced transient cavitation bubbles that mechanically denature DNA by generating violent shock waves locally in solution. I would like to know ...
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Maximum parsimony tree - Am I right, or is the correction model right?

Alright. Monday we have a test, and now I was making a practise test. We have to make a maximum parsimony tree. We must do that monday again, so I want to know if I am thinking wrong, or if the ...
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Human Papillomavirus E7 (HR HPV16)

So there's a protein that binds to E7 viral protein, I want to remove a sub domain of the protein to see which exact domain the E7 binds to. What is the procedure for this? Edit: I believe the virus ...
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501 views

Understanding PAM and BLOSUM matrices

This question might be silly but I need some clarification. I'm slightly confused about if there are multiple PAM and BLOSUM matrices? Is there a different matrix for each sequence? My ...
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484 views

Could a 3D Printed Plant Seed be Possible with Existing Technology?

The first genetically cloned animal was Dolly the sheep. As I understand it, this was possible because all that was needed was an embryo containing the cloned genetic material and a womb for that ...
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Is there a method to isolate half of the chromosomes of a cell?

Each cell has 2N number of chromosomes, I wonder if currently there is a technique allows isolation of N number of chromosomes out ?
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How to design a ChIP-exo experiment with controls?

Does anyone have any ideas on how to run a control/input sample for a ChIP-exo experiment? Is it even necessary to run a control (similar to input DNA for ChIP-seq)? I'm looking for any references ...
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Creating BLAST database with nucleotide "place holder"

I have a set of nucleotide sequences that contain some special characters with multiple meanings: H -> C, A or T K -> G or T M -> C or A R -> G or A S -> C or G W -> A or T Y -> c or T I would like ...
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What is the difference between RFLP and DNA fingerprinting?

Is RFLP (restriction fragment length polymorphism) analysis the same as DNA fingerprinting? I looked for information online and I don't understand the difference.
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Aptamers for DNA

I know that aptamers have a high affinity for their target and are typically made of oligonucleotide s, but can I target DNA using aptamers? If not, what possible technologies can target DNA strands?
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DNA genetic testing from dried sweat crystals?

My sons' dad died and I wanted to do any sort of genetic testing possible, as a gift to my sons. The only item available is dried, crystallized sweat from the bridge of his Oakleys, sadly. Would ...
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Quantifying the number of fragments from RAD library

I have a series of single-end reads from a RAD library of 48 uniquely tagged individuals in fastaq format. The data comes from a small MiSeq run. I want to know the number of unique fragments per ...
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218 views

Is blunt end repair and A-tailing necessary when adaptors can be custom made?

I'm planning on creating a RADseq library, which naturally involves digesting genomic DNA following P1 adaptor ligation. I've read a few protocols that require any over-hangs resulting from ...
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mtDNA sequencing error rates

What is the method to estimate the error rate in mtDNA sequencing? E.g. we are given a profile like this: 16069T 16126C 73G 152C Is there a method, a table of known values, or any other way to say ...
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53 views

Estimating RNA concentration from Specific Activity of Labeled RNA

The question reads, Using T7 RNA polymerase to transcribe in vitro a 100-nt RNA off a DNA template. This RNA contains 19 Adenosines. In your 100 uL transcription reaction you added 1.00 µL of α32P•[...
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4k views

Construct a restriction map of a linear fragment of DNA using the following data?

I've attempted to do the single digests, and the double digests, but cannot complete the map.... I've attached what I've done so far DNA Sizes of Fragments (bp) uncut DNA 900 DNA cut with EcoRI ...
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Hydrogen bonding and the blocking thereof in nucleic acids during nuclear processes

In transcription, RNA polymerase unwinds the DNA double helix and begins attaching RNA nucleotides to the template strand. In its wake, the DNA double helix closes back—this is only natural, seeing as ...
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Infer type of nucleic acid based on number of nucleosides

Let's say we analysed a nucleic acid and found out that it had 20% adenosine, 25% guanosine, 40% thymidine and 15% cytidine. We know that A always pairs with T and G with C. So, based on these ...
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Was the frequency of mutations more during primitive earth due to radioactivity?

Primitive earth was more radioactive (or was it really?) according to radiometric analysis of C14 which suddenly appeared at 4250 million years in the Hadeon eon. Is it possible that ancient high ...
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Is DNA transcription inactive during mitosis ie no proteins are made? How does the cell survive?

I've read that during mitosis, DNA exists as heterochromatin, a form that is unable to be accessed for transcription. Does this mean no new proteins are made during what can be 20% of a cell's life? ...
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Where can one find completed and processed Hi-C datasets?

I and a statistics graduate student at UCR, and I am working on Optimal Binning schemes and peak detection in Hi-C data analysis (a dataset that conveys information about proximity of a DNA strand ...
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What are the effects of non-ultraviolet light radiation on DNA?

I am trying better understand the effects of varying the frequency of light on DNA, however, most of what comes up is "UV light" and how it is damaging to DNA (presumably by ionization). Have there ...
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Insertion of synthetic DNA sequence

If I have some synthetic DNA sequence (<=20 bp long), is there a way for me to reliably insert this sequence next to some n-bp motif? I'd like for this to be possible in humans. If so, are there ...
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How do cell repair mechanism ratios change as they age?

I have seen that embryonic stem cells are shown to use homologous repair for double strand breaks rather then non-homologous end joining (NHEJ). [1] I am wondering if something also happens to a cell'...
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What is the aqueous solution for DNA immobilization?

This paper Electric-field assisted immobilization and hybridization of DNA oligomers on thin-film microchips Which is talking about how the electric field improve the DNA immobilization process. ...